RetrogeneDB ID: | retro_mdom_1197 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 3:444668878..444669525(-) | ||
| Located in intron of: | ENSMODG00000001959 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSMODG00000018439 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_mdom_1197
GCCACTCCAGGTCGCTGGTTTCAGCACCATGCCCTCTGCTGGGGATAGGAGCTTCAGAGTAGCCCTGGAAGGAGCTACGC
AGCCAGCTTTGCTCAGACCTCTCCACCATTTGGATTCCTCTTTGACATTAATGGTGTTTTTATCCATGGCCACAGAGTGA
TCCCTGCTGCCTTGGAAGCTGCCCAAAAGCTGGTTGACTCACATGAGCATTTCCAAATGCCGGTTGTCTTTGTCACTAAT
GCTGGAAATTGTGCACCAAATGTAAAAGCTCAGGAATTGTCAGACCTTCTGGGTCTGAAGGTTGACCCAGAACAAGTAAT
ACTTTCCACCAGTCCCTTGAAATTCTTCTCAAAGTTCCATAATAAGTGAATGCTGGTATGGGGCAGGGGCCTATGATGGG
CAATGCCCAGAACTTGGGCTTCCAGAATGTGGTTACTATTGATGAATTGAGATCTGCATTTCCTCTGCTTGACATGGTTG
ATCTTGAACAATGGCCAAAGACTATGCCTCCCTTGACATCTGCCCTCCCCCCCCTCCCAATAGAAGGGGTACTTCTCTTC
AGAGAGCTAGTCAGCTAGGAGACAAGTCTCCAGCTCATCATGGATGTCCTCAGCAATAGGAACCCTGGCACAGGGCTGCT
AGTAGCC
ORF - retro_mdom_1197 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 80.73 % |
| Parental protein coverage: | 58.9 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | AAPGRWLRHRALCRGWELQGSPGRSYAAGLAQTSPTFGFLFDIDGVFIRGHKVIPAALEAARKLVDSHGH |
| A.PGRW..H.ALC.G.ELQ.SPGRSYAA..AQTSP.FGFLFDI.GVFI.GH.VIPAALEAA.KLVDSH.H | |
| Retrocopy | ATPGRWFQHHALCWG*ELQSSPGRSYAASFAQTSPPFGFLFDINGVFIHGHRVIPAALEAAQKLVDSHEH |
| Parental | FRMPVVFVTNAGNCAPHVKAQELSDLLGLQVDPEQVILSSSPLKFFSKFHNKRMLV-SGQGPMVDNARNL |
| F.MPVVFVTNAGNCAP.VKAQELSDLLGL.VDPEQVILS.SPLKFFSKFHNK.MLV..GQGPM..NA.NL | |
| Retrocopy | FQMPVVFVTNAGNCAPNVKAQELSDLLGLKVDPEQVILSTSPLKFFSKFHNK*MLV<MGQGPMMGNAQNL |
| Parental | GFQNVVTIEELRSAFPVLDMVDLERRPKTMPPLTS--DFPPIEGVLLFGEPVRWETNLQLIMDVLLSNGN |
| GFQNVVTI.ELRSAFP.LDMVDLE..PKTMPPLTS.....PIEGVLLF.E.V..ET.LQLIMDV.LSN.N | |
| Retrocopy | GFQNVVTIDELRSAFPLLDMVDLEQWPKTMPPLTSAXXXXPIEGVLLFRELVS*ETSLQLIMDV-LSNRN |
| Parental | PGTGLAVA |
| PGTGL.VA | |
| Retrocopy | PGTGLLVA |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
Expression validation based on RNA-Seq data:
| Library | Retrocopy expression | Parental gene expression |
|---|---|---|
| SRP007412_brain | 0 .00 RPM | 0 .00 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 0 .00 RPM |
| SRP007412_heart | 0 .00 RPM | 0 .00 RPM |
| SRP007412_kidney | 0 .00 RPM | 0 .00 RPM |
| SRP007412_liver | 0 .00 RPM | 0 .00 RPM |
| SRP007412_testis | 0 .00 RPM | 0 .00 RPM |
Monodelphis domestica was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mdom_1197 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1197 was not experimentally validated.
Retrocopy orthology:
Monodelphis domestica does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Monodelphis domestica | ENSMODG00000018439 | 1 retrocopy |
retro_mdom_1197 ,
|
| Otolemur garnettii | ENSOGAG00000009307 | 1 retrocopy |